DNA Overlap Catenation by XPCR: A Theoretical Analysis

This paper proposes and investigates overlap catenation as a formal model of a special case of cross-pairing PCR, an experimental procedure used to recombine two DNA strands by using the DNA Polymerase enzyme. This study is part of ongoing efforts to provide a formal framework and rigorous treatment of DNA-based information and DNA-based computation. Other studies along these lines include theoretical explorations of splicing systems, insertion/deletion systems, substitution, hairpin extension, hairpin reduction, contextual intraand intermolecular recombinations, and template-guided recombination in cellular computation, as well as directed extension by PCR. In this context, we formally define and investigate overlap catenation and its properties: closure properties of basic language families under this operation, decision problems, as well as the possible use of iterated overlap catenation to generate DNA libraries.